Bruce Willis' character is Joseph ColtonIn the latest trailer, he calls himself Joe.
Doctor Venom will appear.Bonus points if he's played by Michael Emerson, thus making it the second time he's portrayed the character.
Even when Cobra's exposed, several military and political officials will STILL side with Cobra's regime.Jossed. (Unless the third movie says otherwise.)
Duke isn't dead.He's just in a coma.
Third Movie charactersJoes: Shipwreck (US Navy Special Warfare Combatant-craft Crewman) Gung-Ho (US Marine) Slaughter A former Cobra Viper. Lt. Falcon Cobra: Major Bludd (Former Special Air Service Regiment) Overkill (A Viper) Blackout (A Joe who defected to Cobra a month before Retaliation) Dr Mindbender (A former MARS scientist who was a colleague of Cobra Commander when he used to be just the Doctor)
Zartan isn't dead.The nanomites heal Zartan's face when he cuts it with a knife. Being stabbed through the chest is more serious than a cut on the face, but who's to say they can't heal that. It might just take longer.
Destro isn't dead.It was never confirmed that he died it the explosion.
Scarlett isn't dead.She's just hiding. Or on another mission that precluded her being called back, or something.
If there's a third movie, Cobra Commander will be revealed to have been running a Xanatos Gambit.If you look at events, in the first movie his plan mostly works. He gets Zartan into the White House undetected. Perhaps getting captured was even part of his plan. If the world isn't looking for Cobra Commander, they don't suspect his plan is still in place. He even says he never had a doubt when Storm Shadow rescued him; indicating that he planned on being captured and rescued. So what did he accomplish in this movie? He got the GI Joes mostly killed and destroyed the world's nuclear arsenal completely. He even devastated most of London and had Destro killed. He also had his escape really handy for a guy who was about to take over the world. As the third movie unfolds, it will probably become clear that all he was after was nuclear disarmament; and that leads into his next plan. He also leaves the Zeus controller with Firefly to be chased and intercepted when he could have easily taken it on the helicopter he escaped on and had all of the rods destroy the targets; indicating he didn't want them to go off at all.
The Zeus weapon used Red Matter to destroy London.Because it caused a seismic event similar to the ones before Vulcan was destroyed.
G.I. Joe was heavily downsized and absorbed into the US military between films.Most of the Joes found new careers. The ones who remained were turned into a small American unit doing American things (like we see at the beginning of Retaliation.) The Pit was given to the Egyptian government, Breaker was allowed to return to French territory, etc. This explains the discrepancy between the way the organization is depicted in the two films, and means that Scarlett, General Hawk, Ripcord, etc. are still alive.
Destro will return but will not rejoin Cobra.He'll be the leader of his own third-party faction, with a surprise agenda. Also, he'll probably be recast.
The G.I. Joe: The Rise of Cobra Baroness will not return.Sienna Miller does not want to return to the role. If we see the Baroness again in this series, it will be a different individual using the name and look (maybe a Russian).
Practically 95% of the Joes were wiped out prior to the film.How? Remember the "nanobyte wars" mentioned in the beginning, it could have ended badly for the Joes, hence no Hawk, Ripcord, Scarlet, Heavy Duty, Stone, Breaker, Anna/Baroness, Pit, and carrier where Anna/Baroness was imprisoned. Also explains why the Joes seen in the movie are small enough that after getting bombed by Cobras, they're considered dead.